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Coexpression cluster:C1161: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!1.06e-50!115;UBERON:0001049!1.39e-43!57;UBERON:0005068!1.39e-43!57;UBERON:0006241!1.39e-43!57;UBERON:0007135!1.39e-43!57;UBERON:0000955!9.68e-38!69;UBERON:0006238!9.68e-38!69;UBERON:0001017!2.80e-37!82;UBERON:0002616!8.61e-37!59;UBERON:0005743!5.61e-36!86;UBERON:0000073!1.46e-34!94;UBERON:0001016!1.46e-34!94;UBERON:0003080!2.47e-34!42;UBERON:0002780!1.03e-33!41;UBERON:0001890!1.03e-33!41;UBERON:0006240!1.03e-33!41;UBERON:0002346!2.01e-32!90;UBERON:0003075!7.85e-31!86;UBERON:0007284!7.85e-31!86;UBERON:0002020!4.27e-27!34;UBERON:0003528!4.27e-27!34;UBERON:0001893!5.37e-27!34;UBERON:0002791!5.01e-26!33;UBERON:0001869!8.94e-25!32;UBERON:0000033!8.94e-23!123;UBERON:0000924!2.17e-22!173;UBERON:0006601!2.17e-22!173;UBERON:0000153!3.68e-22!129;UBERON:0007811!3.68e-22!129;UBERON:0003056!3.78e-22!61;UBERON:0004121!5.15e-21!169;UBERON:0002619!9.09e-20!22;UBERON:0000956!7.96e-18!25;UBERON:0000203!7.96e-18!25;UBERON:0001950!8.97e-18!20;UBERON:0000475!1.07e-13!365;UBERON:0002308!4.71e-11!9;UBERON:0000125!4.71e-11!9;UBERON:0002420!6.76e-11!9;UBERON:0007245!6.76e-11!9;UBERON:0010009!6.76e-11!9;UBERON:0010011!6.76e-11!9;UBERON:0000454!6.76e-11!9;UBERON:0003076!3.05e-10!15;UBERON:0003057!3.05e-10!15;UBERON:0002298!1.35e-09!8;UBERON:0009663!6.93e-09!7;UBERON:0004732!2.75e-08!13;UBERON:0001894!3.72e-08!7;UBERON:0006222!3.72e-08!7;UBERON:0000200!9.00e-08!6;UBERON:0004733!1.96e-07!12;UBERON:0002028!1.96e-07!12;UBERON:0007277!1.96e-07!12;UBERON:0001871!3.21e-07!7;UBERON:0000483!5.70e-07!309;UBERON:0000025!5.81e-07!194
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}}
}}

Revision as of 16:57, 8 August 2012


Full id: C1161_osteosarcoma_Melanocyte_cerebellum_substantia_thalamus_globus_occipital



Phase1 CAGE Peaks

Hg19::chr12:110510751..110510754,-p@chr12:110510751..110510754
-
Hg19::chr12:110511424..110511445,-p5@C12orf76
Hg19::chr13:113698946..113698993,+p1@MCF2L
Hg19::chr13:113698996..113699013,+p6@MCF2L
Hg19::chr13:113699029..113699040,+p11@MCF2L
Hg19::chr16:27730331..27730353,+p@chr16:27730331..27730353
+
Hg19::chr8:112039622..112039629,-p1@ENST00000523557


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0332038149063935
GO:0035023regulation of Rho protein signal transduction0.0332038149063935
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0332038149063935
GO:0007266Rho protein signal transduction0.0332038149063935
GO:0005085guanyl-nucleotide exchange factor activity0.0372071117390792
GO:0046578regulation of Ras protein signal transduction0.0372071117390792
GO:0007265Ras protein signal transduction0.0372071117390792
GO:0005083small GTPase regulator activity0.0372071117390792
GO:0051056regulation of small GTPase mediated signal transduction0.0372071117390792
GO:0030695GTPase regulator activity0.049452490286118



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
skin fibroblast2.25e-0823
Uber Anatomy
Ontology termp-valuen
adult organism1.06e-50115
neural tube1.39e-4357
neural rod1.39e-4357
future spinal cord1.39e-4357
neural keel1.39e-4357
brain9.68e-3869
future brain9.68e-3869
central nervous system2.80e-3782
regional part of brain8.61e-3759
regional part of nervous system1.46e-3494
nervous system1.46e-3494
anterior neural tube2.47e-3442
regional part of forebrain1.03e-3341
forebrain1.03e-3341
future forebrain1.03e-3341
neurectoderm2.01e-3290
neural plate7.85e-3186
presumptive neural plate7.85e-3186
gray matter4.27e-2734
brain grey matter4.27e-2734
telencephalon5.37e-2734
regional part of telencephalon5.01e-2633
cerebral hemisphere8.94e-2532
head8.94e-23123
ectoderm2.17e-22173
presumptive ectoderm2.17e-22173
anterior region of body3.68e-22129
craniocervical region3.68e-22129
pre-chordal neural plate3.78e-2261
ectoderm-derived structure5.15e-21169
regional part of cerebral cortex9.09e-2022
cerebral cortex7.96e-1825
pallium7.96e-1825
neocortex8.97e-1820
organism subdivision1.07e-13365
nucleus of brain4.71e-119
neural nucleus4.71e-119
basal ganglion6.76e-119
nuclear complex of neuraxis6.76e-119
aggregate regional part of brain6.76e-119
collection of basal ganglia6.76e-119
cerebral subcortex6.76e-119
posterior neural tube3.05e-1015
chordal neural plate3.05e-1015
brainstem1.35e-098
telencephalic nucleus6.93e-097
segmental subdivision of nervous system2.75e-0813
diencephalon3.72e-087
future diencephalon3.72e-087
gyrus9.00e-086
segmental subdivision of hindbrain1.96e-0712
hindbrain1.96e-0712
presumptive hindbrain1.96e-0712
temporal lobe3.21e-077
epithelium5.70e-07309
tube5.81e-07194


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.